1 Setup

source("functions.R")
source("functions_sam.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)
sample <- c("joint_cortex.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(paste0("figures", "/", "5.1-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_beam_analysis", "/"))

1.1 Load Monocle object

load(file.path(monocle_objects_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11.Rda"))

1.2 Read transcription factors.

input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())

2 BEAM analysis

# Reset root state for BEAM analysis
beam_results <- BEAM(monocle, branch_point = 3, cores = 12)
beam_results <- rownames_to_column(beam_results, "gene")
beam_results <- beam_results %>% select(-gene_short_name)
beam_results %>% slice(1:20) %>% kable() %>% kable_styling()
gene status family pval qval num_cells_expressed use_for_ordering
Xkr4 OK negbinomial.size 0.0762506 0.1461906 11 FALSE
Sox17 OK negbinomial.size 0.0352186 0.0758082 23 FALSE
Mrpl15 OK negbinomial.size 0.0909183 0.1690080 1940 FALSE
Lypla1 OK negbinomial.size 0.1483227 0.2514979 1490 FALSE
Tcea1 OK negbinomial.size 0.0678570 0.1325969 2129 FALSE
Rgs20 OK negbinomial.size 0.0000000 0.0000000 1615 FALSE
Atp6v1h OK negbinomial.size 0.0008580 0.0027079 1382 FALSE
Oprk1 OK negbinomial.size 0.8594185 0.9686370 18 FALSE
Rb1cc1 OK negbinomial.size 0.1235794 0.2170257 1642 FALSE
4732440D04Rik OK negbinomial.size 0.4398759 0.5905570 145 FALSE
St18 OK negbinomial.size 0.0674713 0.1319679 46 FALSE
Pcmtd1 OK negbinomial.size 0.0000002 0.0000012 2317 FALSE
Gm26901 OK negbinomial.size 0.0709320 0.1376650 42 FALSE
Sntg1 OK negbinomial.size 0.1050835 0.1900523 31 FALSE
Rrs1 OK negbinomial.size 0.0000000 0.0000000 1919 FALSE
Adhfe1 OK negbinomial.size 0.0000000 0.0000000 1765 FALSE
3110035E14Rik OK negbinomial.size 0.0238844 0.0544904 173 FALSE
Mybl1 OK negbinomial.size 0.8937557 0.9962243 61 FALSE
Vcpip1 OK negbinomial.size 0.8175322 0.9327956 1052 FALSE
1700034P13Rik OK negbinomial.size 0.0296821 0.0656779 25 FALSE 
write.table(beam_results, file.path(tables_directory, "5.1-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_beam_results.txt"), sep="\t", quote=FALSE, row.names=FALSE)

2.1 q value < 5*10^-5 (plot_genes_branched_heatmap)

significant_genes_q_value_5_10_minus_5 <- filter(beam_results, qval < 5*10^-5) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes:  4521
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 226
plot_genes_branched_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], branch_labels=c("Ependymal cells", "Astrocytes"), cluster_rows=TRUE, num_clusters=6, show_rownames = TRUE)

plot_genes_branched_heatmap_output_q_value_5_10_minus_5 <- plot_genes_branched_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], branch_labels=c("Ependymal cells", "Astrocytes"), cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_branched_heatmap_output_q_value_5_10_minus_5[["ph_res"]], file.path("figures", "5.1-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_beam_analysis", "beam_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf 
##   2
heatmap_matrix_ori_q_value_5_10_minus_5 <- plot_genes_branched_heatmap_output_q_value_5_10_minus_5[["heatmap_matrix_ori"]]
ph_res_q_value_5_10_minus_5 <- plot_genes_branched_heatmap_output_q_value_5_10_minus_5[["ph_res"]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_ori_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])

transcription_factors_table_q_value_5_10_minus_5 <- filter(beam_results, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))

write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "5.1-significant_transcription_factors_beam_analysis_qval_5_10_minus_5_plot_genes_branched_heatmap.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_ori_q_value_5_10_minus_5 <- plot_genes_branched_heatmap_output_q_value_5_10_minus_5[["heatmap_matrix_ori"]]
heatmap_matrix_ori_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_ori_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_ori_q_value_5_10_minus_5 <- heatmap_matrix_ori_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_ori_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 100 99 98 97 96 95 94 93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 77 76 75 74 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200
Foxa2 2.1879345 1.8330830 1.5134764 1.2264464 0.9693410 0.7395731 0.5346582 0.3522412 0.1901148 0.0462305 -0.0812973 -0.1941905 -0.2940117 -0.3821700 -0.4599290 -0.5284161 -0.5886320 -0.6414604 -0.6876775 -0.7279610 -0.7629031 -0.7931133 -0.8192016 -0.8416821 -0.8609858 -0.8774739 -0.8914500 -0.9031689 -0.9128448 -0.9206570 -0.9267555 -0.9312654 -0.9342898 -0.9359137 -0.9362055 -0.9352198 -0.9329990 -0.9295746 -0.9249685 -0.9191946 -0.9122590 -0.9041617 -0.8948969 -0.8844538 -0.8728176 -0.8599701 -0.8458903 -0.8305552 -0.8139410 -0.7960230 -0.7767775 -0.7561821 -0.7342169 -0.7108655 -0.6861166 -0.6599645 -0.6324113 -0.6034675 -0.5731542 -0.5415040 -0.5085631 -0.4743926 -0.4390699 -0.4026907 -0.3653700 -0.3272437 -0.2884693 -0.2492274 -0.2097218 -0.1701800 -0.1308528 -0.0920143 -0.0539600 -0.0170059 0.0185144 0.0523219 0.0843226 0.1144682 0.1427269 0.1690826 0.1935346 0.2160971 0.2367981 0.2556790 0.2727933 0.2882059 0.3019917 0.3142352 0.3250289 0.3344728 0.3426731 0.3497414 0.3557939 0.3609506 0.3653347 0.3690718 0.3722896 0.3751171 0.3776846 0.3801236 0.7655511 0.6820075 0.6021086 0.5260661 0.4540417 0.3861532 0.3224817 0.2630782 0.2079691 0.1571633 0.1106573 0.0684411 0.0305032 -0.0031638 -0.0325586 -0.0576658 -0.0784511 -0.0948559 -0.1067913 -0.1141325 -0.1167112 -0.1143078 -0.1066422 -0.0933628 -0.0740331 -0.0481156 -0.0150431 0.0253258 0.0729932 0.1279982 0.1903993 0.2602568 0.3376136 0.4224759 0.5147911 0.6144259 0.7211417 0.8345707 0.9541902 1.0792987 1.2089936 1.3421512 1.4774116 1.6131706 1.7475779 1.8785464 2.0037718 2.1207651 2.2268982 2.3194632 2.3957450 2.4531059 2.4890804 2.5014761 2.4884793 2.4487571 2.3815526 2.2867673 2.1650217 2.0176914 1.8469091 1.6555314 1.4470656 1.2255578 0.9954441 0.7613740 0.5280126 0.2998374 0.0809433 -0.1251298 -0.3155320 -0.4881909 -0.6418471 -0.7760344 -0.8910127 -0.9876615 -1.0673460 -1.1317726 -1.1828438 -1.2225271 -1.2527420 -1.2752450 -1.2916259 -1.3032981 -1.3114509 -1.3170408 -1.3208079 -1.3233063 -1.3249388 -1.3259910 -1.3266608 -1.3270823 -1.3273448 -1.3275067 -1.3276058 -1.3276660 -1.3277023 -1.3277241 -1.3277372 -1.3277450
Zbtb10 2.5934131 2.2889140 2.0048080 1.7404038 1.4949248 1.2675329 1.0573504 0.8634782 0.6850123 0.5210566 0.3707345 0.2331977 0.1076337 -0.0067288 -0.1106158 -0.2047043 -0.2896207 -0.3659388 -0.4341788 -0.4948068 -0.5482419 -0.5950286 -0.6358107 -0.6711510 -0.7015350 -0.7273816 -0.7490529 -0.7668610 -0.7810754 -0.7919283 -0.7996194 -0.8043203 -0.8061778 -0.8053173 -0.8018454 -0.7958525 -0.7874149 -0.7765967 -0.7634516 -0.7480246 -0.7303537 -0.7104709 -0.6884040 -0.6641778 -0.6378156 -0.6093402 -0.5787754 -0.5461474 -0.5114859 -0.4748257 -0.4362080 -0.3956817 -0.3533050 -0.3091466 -0.2632873 -0.2158214 -0.1668578 -0.1165217 -0.0649557 -0.0123209 0.0412020 0.0954116 0.1500856 0.2049799 0.2598285 0.3143435 0.3682155 0.4211147 0.4726916 0.5225786 0.5703924 0.6157363 0.6582031 0.6973785 0.7328456 0.7642951 0.7917155 0.8151663 0.8347305 0.8505121 0.8626348 0.8712398 0.8764837 0.8785365 0.8775794 0.8738034 0.8674067 0.8585936 0.8475721 0.8345530 0.8197480 0.8033687 0.7856252 0.7667251 0.7468729 0.7262690 0.7051092 0.6835843 0.6618796 0.6401752 1.5792840 1.4003745 1.2308312 1.0707191 0.9200197 0.7786450 0.6464506 0.5232478 0.4088146 0.3029060 0.2052630 0.1156211 0.0337174 -0.0407025 -0.1078787 -0.1680314 -0.2213557 -0.2680167 -0.3081451 -0.3418318 -0.3691229 -0.3900141 -0.4044442 -0.4122880 -0.4133472 -0.4073402 -0.3939790 -0.3734151 -0.3459249 -0.3117290 -0.2710086 -0.2239198 -0.1706089 -0.1112261 -0.0459393 0.0250509 0.1014979 0.1830943 0.2694574 0.3601158 0.4544957 0.5519085 0.6515408 0.7524456 0.8535376 0.9535915 1.0512455 1.1450102 1.2332830 1.3143699 1.3865138 1.4479300 1.4968487 1.5315633 1.5504837 1.5521934 1.5355078 1.4995319 1.4437131 1.3678888 1.2723226 1.1577284 1.0252782 0.8765922 0.7137098 0.5390408 0.3552974 0.1654112 -0.0275649 -0.2205612 -0.4105995 -0.5948973 -0.7709628 -0.9366732 -1.0903347 -1.2307171 -1.3570651 -1.4690841 -1.5669052 -1.6510313 -1.7222641 -1.7815366 -1.8299550 -1.8688327 -1.8995555 -1.9234772 -1.9418493 -1.9557807 -1.9662213 -1.9739612 -1.9796423 -1.9837742 -1.9867547 -1.9888886 -1.9904061 -1.9914790 -1.9922335 -1.9927619 -1.9931305 -1.9933869
Zbtb5 1.2518322 1.1545388 1.0590245 0.9655424 0.8743289 0.7856044 0.6995745 0.6164310 0.5363530 0.4595082 0.3860541 0.3161393 0.2499051 0.1874867 0.1290144 0.0746158 0.0244166 -0.0214574 -0.0628786 -0.0997162 -0.1318426 -0.1593082 -0.1823369 -0.2011454 -0.2159366 -0.2269010 -0.2342181 -0.2380581 -0.2385823 -0.2359452 -0.2302947 -0.2217737 -0.2105207 -0.1966707 -0.1803562 -0.1617078 -0.1408549 -0.1179266 -0.0930518 -0.0663608 -0.0379846 -0.0080565 0.0232881 0.0559107 0.0896701 0.1244211 0.1600148 0.1962982 0.2331138 0.2702995 0.3076886 0.3451097 0.3823863 0.4193373 0.4557768 0.4915145 0.5263555 0.5601012 0.5925489 0.6234928 0.6527243 0.6800325 0.7052050 0.7280281 0.7482884 0.7657729 0.7802704 0.7915722 0.7994731 0.8037727 0.8042766 0.8007974 0.7931557 0.7811822 0.7647182 0.7437070 0.7183431 0.6888679 0.6555280 0.6185741 0.5782592 0.5348374 0.4885629 0.4396884 0.3884643 0.3351378 0.2799518 0.2231440 0.1649467 0.1055857 0.0452799 -0.0157590 -0.0773269 -0.1392279 -0.2012740 -0.2632854 -0.3250908 -0.3865272 -0.4474397 -0.5076816 -0.2799539 -0.2553612 -0.2306245 -0.2057282 -0.1806564 -0.1553929 -0.1299212 -0.1042245 -0.0782856 -0.0520869 -0.0256105 0.0011618 0.0282487 0.0556691 0.0834424 0.1115884 0.1401273 0.1690798 0.1984668 0.2283100 0.2586312 0.2894529 0.3207981 0.3526903 0.3851534 0.4182120 0.4518706 0.4860089 0.5204568 0.5550396 0.5895782 0.6238892 0.6577848 0.6910730 0.7235577 0.7550389 0.7853134 0.8141746 0.8414132 0.8668179 0.8901756 0.9112725 0.9298944 0.9458277 0.9588605 0.9687829 0.9753887 0.9784758 0.9778480 0.9733155 0.9646963 0.9518179 0.9345178 0.9126453 0.8860625 0.8546459 0.8182873 0.7768954 0.7303969 0.6787373 0.6218827 0.5598203 0.4925593 0.4201322 0.3425948 0.2600273 0.1725347 0.0802465 -0.0166826 -0.1180735 -0.2237224 -0.3334017 -0.4468609 -0.5638272 -0.6840072 -0.8070880 -0.9327388 -1.0606134 -1.1903514 -1.3215810 -1.4539128 -1.5867616 -1.7193894 -1.8511132 -1.9813151 -2.1094432 -2.2350113 -2.3575976 -2.4768427 -2.5924467 -2.7041667 -2.8118123 -2.9152426 -3.0000000 -3.0000000 -3.0000000 -3.0000000 -3.0000000 -3.0000000 -3.0000000
Lcorl 0.3272389 0.2856412 0.2444367 0.2037104 0.1635451 0.1240207 0.0852150 0.0472036 0.0100595 -0.0261458 -0.0613431 -0.0954649 -0.1284451 -0.1602194 -0.1907246 -0.2198986 -0.2476803 -0.2740094 -0.2988259 -0.3220704 -0.3436858 -0.3636694 -0.3820722 -0.3989455 -0.4143387 -0.4282994 -0.4408735 -0.4521054 -0.4620381 -0.4707132 -0.4781711 -0.4844509 -0.4895909 -0.4936282 -0.4965991 -0.4985391 -0.4994830 -0.4994648 -0.4985181 -0.4966757 -0.4939702 -0.4904338 -0.4860980 -0.4809944 -0.4751543 -0.4686086 -0.4613882 -0.4535240 -0.4450467 -0.4359871 -0.4263759 -0.4162441 -0.4056226 -0.3945426 -0.3830353 -0.3711323 -0.3588653 -0.3462662 -0.3333675 -0.3202016 -0.3068015 -0.2932004 -0.2794320 -0.2655301 -0.2515291 -0.2374638 -0.2233693 -0.2092811 -0.1952351 -0.1812676 -0.1674152 -0.1537150 -0.1402045 -0.1269215 -0.1139039 -0.1011784 -0.0887393 -0.0765754 -0.0646757 -0.0530288 -0.0416230 -0.0304466 -0.0194880 -0.0087350 0.0018245 0.0122026 0.0224118 0.0324645 0.0423734 0.0521511 0.0618105 0.0713645 0.0808262 0.0902086 0.0995250 0.1087887 0.1180132 0.1272120 0.1363986 0.1455868 -0.0708136 -0.0432412 -0.0154949 0.0124556 0.0406417 0.0690951 0.0978483 0.1269343 0.1563870 0.1862409 0.2165311 0.2472937 0.2785654 0.3103837 0.3427869 0.3758142 0.4095058 0.4439027 0.4790468 0.5149812 0.5517499 0.5893981 0.6279720 0.6675193 0.7080886 0.7497301 0.7924703 0.8361851 0.8806895 0.9257936 0.9713014 1.0170115 1.0627167 1.1082039 1.1532545 1.1976440 1.2411426 1.2835153 1.3245225 1.3639200 1.4014598 1.4368908 1.4699591 1.5004090 1.5279839 1.5524272 1.5734832 1.5908980 1.6044214 1.6138071 1.6188150 1.6192118 1.6147729 1.6052836 1.5905407 1.5703543 1.5445488 1.5129649 1.4754611 1.4319153 1.3822260 1.3263142 1.2641245 1.1956266 1.1208164 1.0397173 0.9523809 0.8588882 0.7593498 0.6539068 0.5427306 0.4260234 0.3040177 0.1769757 0.0451887 -0.0910236 -0.2313151 -0.3753144 -0.5226267 -0.6728363 -0.8254977 -0.9799100 -1.1351654 -1.2904100 -1.4448582 -1.5977953 -1.7485780 -1.8966352 -2.0414662 -2.1826399 -2.3197914 -2.4526195 -2.5808826 -2.7043950 -2.8230226 -2.9366784 -3.0000000 -3.0000000 -3.0000000 -3.0000000
Gm14295 -1.2564472 -1.1928450 -1.1279752 -1.0619281 -0.9948033 -0.9267101 -0.8577679 -0.7881061 -0.7178650 -0.6471952 -0.5762585 -0.5052272 -0.4342848 -0.3636252 -0.2934530 -0.2239831 -0.1554400 -0.0880578 -0.0220793 0.0422448 0.1046599 0.1649847 0.2231178 0.2789653 0.3324375 0.3834487 0.4319181 0.4777696 0.5209318 0.5613386 0.5989291 0.6336478 0.6654445 0.6942748 0.7200998 0.7428863 0.7626069 0.7792400 0.7927697 0.8031859 0.8104843 0.8146663 0.8157390 0.8137150 0.8086124 0.8004550 0.7892715 0.7750961 0.7579680 0.7379312 0.7150346 0.6893314 0.6608797 0.6297412 0.5959822 0.5596725 0.5208855 0.4796981 0.4361904 0.3904453 0.3425485 0.2925881 0.2406545 0.1868401 0.1312390 0.0739467 0.0150601 -0.0453229 -0.1071036 -0.1701829 -0.2344614 -0.2998394 -0.3662176 -0.4334970 -0.5015792 -0.5703506 -0.6396581 -0.7093473 -0.7792704 -0.8492864 -0.9192609 -0.9890667 -1.0585839 -1.1276992 -1.1963070 -1.2643083 -1.3316115 -1.3981317 -1.4637908 -1.5285176 -1.5922469 -1.6549203 -1.7164851 -1.7768947 -1.8361077 -1.8940886 -1.9508066 -2.0062358 -2.0603551 -2.1131474 -2.4032891 -2.3180980 -2.2288456 -2.1355010 -2.0380554 -1.9365247 -1.8309527 -1.7214140 -1.6080168 -1.4909060 -1.3702660 -1.2463233 -1.1193490 -0.9896608 -0.8576251 -0.7236578 -0.5882260 -0.4518474 -0.3150910 -0.1785750 -0.0429661 0.0910239 0.2226407 0.3510926 0.4755544 0.5951747 0.7091417 0.8170077 0.9184954 1.0133687 1.1014332 1.1825364 1.2565665 1.3234522 1.3831612 1.4356990 1.4811072 1.5194617 1.5508704 1.5754715 1.5934305 1.6049388 1.6102103 1.6094796 1.6029994 1.5910380 1.5738770 1.5518088 1.5251348 1.4941628 1.4592053 1.4205773 1.3785949 1.3335731 1.2858248 1.2356592 1.1833804 1.1292867 1.0736691 1.0168111 0.9589876 0.9004642 0.8414974 0.7823337 0.7232097 0.6643519 0.6059767 0.5482908 0.4914911 0.4357651 0.3812913 0.3282395 0.2767717 0.2270422 0.1791984 0.1333818 0.0897281 0.0483686 0.0094307 -0.0269614 -0.0606917 -0.0917916 -0.1204330 -0.1467861 -0.1710143 -0.1932747 -0.2137189 -0.2324936 -0.2497409 -0.2655994 -0.2802039 -0.2936865 -0.3061766 -0.3178013 -0.3286857 -0.3389532 -0.3487254 -0.3581229 -0.3672647 -0.3762688
Glmp 0.8063873 0.7852376 0.7642393 0.7434817 0.7230532 0.7030411 0.6835319 0.6646110 0.6463631 0.6288721 0.6122212 0.5964931 0.5817700 0.5681336 0.5556656 0.5444474 0.5345607 0.5260871 0.5191088 0.5137087 0.5099660 0.5078645 0.5072915 0.5081315 0.5102698 0.5135920 0.5179847 0.5233342 0.5295273 0.5364504 0.5439899 0.5520318 0.5604617 0.5691646 0.5780252 0.5869273 0.5957545 0.6043895 0.6127145 0.6206113 0.6279611 0.6346448 0.6405430 0.6455361 0.6495047 0.6523292 0.6538907 0.6540705 0.6527510 0.6498153 0.6451478 0.6386346 0.6301634 0.6196243 0.6069095 0.5919145 0.5745375 0.5546807 0.5322501 0.5071560 0.4793137 0.4486437 0.4150724 0.3785323 0.3389625 0.2963095 0.2505275 0.2015787 0.1494341 0.0940741 0.0354886 -0.0263223 -0.0913477 -0.1595656 -0.2309423 -0.3053692 -0.3825624 -0.4622121 -0.5440127 -0.6276638 -0.7128714 -0.7993493 -0.8868195 -0.9750133 -1.0636726 -1.1525498 -1.2414090 -1.3300264 -1.4181907 -1.5057034 -1.5923789 -1.6780453 -1.7625435 -1.8457279 -1.9274660 -2.0076383 -2.0861378 -2.1628700 -2.2377523 -2.3107134 -2.5171896 -2.4185006 -2.3158767 -2.2093835 -2.0991142 -1.9851925 -1.8677740 -1.7470474 -1.6232360 -1.4965989 -1.3674311 -1.2360640 -1.1028657 -0.9682400 -0.8326256 -0.6964954 -0.5603544 -0.4247379 -0.2902091 -0.1573567 -0.0267918 0.1008555 0.2249390 0.3448006 0.4597739 0.5691881 0.6724259 0.7692041 0.8593897 0.9428824 1.0196126 1.0895405 1.1526541 1.2089682 1.2585223 1.3013798 1.3376256 1.3673651 1.3907227 1.4078400 1.4188746 1.4239986 1.4233973 1.4172676 1.4058170 1.3892623 1.3678283 1.3417465 1.3112542 1.2765935 1.2380099 1.1957516 1.1500685 1.1012110 1.0494296 0.9949740 0.9380917 0.8790283 0.8180260 0.7553232 0.6911541 0.6257481 0.5593290 0.4921151 0.4243184 0.3561445 0.2877922 0.2194534 0.1513127 0.0835477 0.0163285 -0.0501820 -0.1158283 -0.1804620 -0.2439418 -0.3061333 -0.3669087 -0.4261468 -0.4837321 -0.5395552 -0.5935165 -0.6456221 -0.6959779 -0.7446900 -0.7918609 -0.8375894 -0.8819707 -0.9250970 -0.9670570 -1.0079369 -1.0478196 -1.0867855 -1.1249126 -1.1622759 -1.1989486 -1.2350011 -1.2705017 -1.3055167 -1.3401101 -1.3743438
Bhlhe40 0.3277833 0.2935038 0.2597231 0.2265960 0.1942717 0.1628930 0.1325975 0.1035176 0.0757813 0.0495121 0.0248305 0.0018541 -0.0193017 -0.0385227 -0.0556949 -0.0707043 -0.0834353 -0.0937697 -0.1015863 -0.1067590 -0.1091619 -0.1088034 -0.1058258 -0.1003712 -0.0925763 -0.0825736 -0.0704923 -0.0564600 -0.0406026 -0.0230462 -0.0039174 0.0166560 0.0385438 0.0616133 0.0857286 0.1107498 0.1365327 0.1629289 0.1897846 0.2169412 0.2442345 0.2714952 0.2985486 0.3252145 0.3513079 0.3766389 0.4010131 0.4242324 0.4460950 0.4663967 0.4849310 0.5014906 0.5158680 0.5278565 0.5372517 0.5438524 0.5474621 0.5478905 0.5449545 0.5384807 0.5283059 0.5142798 0.4962658 0.4741436 0.4478102 0.4171820 0.3821966 0.3428141 0.2990193 0.2508223 0.1982606 0.1414003 0.0803364 0.0151944 -0.0538695 -0.1265814 -0.2024196 -0.2808310 -0.3612769 -0.4432368 -0.5262126 -0.6097317 -0.6933500 -0.7766545 -0.8592643 -0.9408327 -1.0210473 -1.0996305 -1.1763394 -1.2509650 -1.3233311 -1.3932932 -1.4607368 -1.5255756 -1.5877492 -1.6472216 -1.7039782 -1.7580243 -1.8093824 -1.8580900 -2.0227133 -1.9623083 -1.8967332 -1.8257158 -1.7490030 -1.6663683 -1.5776194 -1.4826077 -1.3812365 -1.2734712 -1.1593478 -1.0389827 -0.9125804 -0.7804418 -0.6429699 -0.5006751 -0.3541777 -0.2042094 -0.0516117 0.1026675 0.2575795 0.4119833 0.5646553 0.7143020 0.8595738 0.9990805 1.1314878 1.2559602 1.3719177 1.4788675 1.5764038 1.6642067 1.7420400 1.8097481 1.8672528 1.9145489 1.9516999 1.9788333 1.9961358 2.0038482 2.0022602 1.9917059 1.9725581 1.9452238 1.9101394 1.8677654 1.8185827 1.7630872 1.7017863 1.6351943 1.5638287 1.4882065 1.4088405 1.3262365 1.2408898 1.1532828 1.0638824 0.9731379 0.8814788 0.7893137 0.6970283 0.6049851 0.5135220 0.4229522 0.3335639 0.2456202 0.1593595 0.0749964 -0.0072786 -0.0872970 -0.1649123 -0.2399981 -0.3124470 -0.3821695 -0.4490922 -0.5131563 -0.5743162 -0.6325379 -0.6877974 -0.7400789 -0.7893791 -0.8358140 -0.8796051 -0.9209630 -0.9600835 -0.9971492 -1.0323302 -1.0657859 -1.0976652 -1.1281076 -1.1572442 -1.1851983 -1.2120857 -1.2380158 -1.2630915 -1.2874102 -1.3110637 -1.3341388 -1.3567174 -1.3788771
Gm6710 -1.7567938 -1.6516424 -1.5452170 -1.4377402 -1.3294473 -1.2205868 -1.1114202 -1.0022219 -0.8932794 -0.7848927 -0.6773742 -0.5710479 -0.4662497 -0.3633259 -0.2626329 -0.1645363 -0.0694100 0.0223649 0.1104014 0.1943074 0.2736956 0.3483648 0.4183088 0.4835403 0.5440816 0.5999651 0.6512318 0.6979319 0.7401236 0.7778731 0.8112539 0.8403465 0.8652380 0.8860215 0.9027957 0.9156647 0.9247371 0.9301263 0.9319493 0.9303268 0.9253829 0.9172444 0.9060404 0.8919023 0.8749633 0.8553580 0.8332222 0.8086924 0.7819059 0.7530001 0.7221124 0.6893803 0.6549407 0.6189297 0.5814828 0.5427344 0.5028177 0.4618648 0.4200059 0.3773700 0.3340842 0.2902740 0.2460628 0.2015722 0.1569218 0.1122293 0.0676102 0.0231780 -0.0209558 -0.0646818 -0.1078924 -0.1504821 -0.1923473 -0.2333862 -0.2734988 -0.3126211 -0.3507818 -0.3880244 -0.4243914 -0.4599246 -0.4946652 -0.5286535 -0.5619294 -0.5945320 -0.6264998 -0.6578709 -0.6886825 -0.7189717 -0.7487746 -0.7781272 -0.8070648 -0.8356223 -0.8638340 -0.8917340 -0.9193557 -0.9467323 -0.9738965 -1.0008804 -1.0277160 -1.0544348 -1.5311726 -1.4272279 -1.3220387 -1.2157628 -1.1085674 -1.0006284 -0.8921306 -0.7832682 -0.6742442 -0.5652706 -0.4565682 -0.3483667 -0.2409039 -0.1344259 -0.0291868 0.0745520 0.1765220 0.2764484 0.3740501 0.4690407 0.5611290 0.6500201 0.7354154 0.8170140 0.8945134 0.9676105 1.0360322 1.0996882 1.1585630 1.2126489 1.2619461 1.3064622 1.3462122 1.3812180 1.4115084 1.4371189 1.4580909 1.4744722 1.4863163 1.4936822 1.4966342 1.4952415 1.4895781 1.4797226 1.4657576 1.4477700 1.4258500 1.4000914 1.3705914 1.3374498 1.3007693 1.2606551 1.2172144 1.1705564 1.1207922 1.0680343 1.0123965 0.9539935 0.8929411 0.8293554 0.7633533 0.6950516 0.6245672 0.5520170 0.4775174 0.4011841 0.3231325 0.2434768 0.1623302 0.0798050 -0.0039882 -0.0889400 -0.1749428 -0.2618904 -0.3496789 -0.4382059 -0.5273714 -0.6170773 -0.7072278 -0.7977295 -0.8884913 -0.9794232 -1.0704366 -1.1614457 -1.2523671 -1.3431204 -1.4336279 -1.5238147 -1.6136087 -1.7029408 -1.7917445 -1.8799562 -1.9675152 -2.0543634 -2.1404458 -2.2257099 -2.3101058 -2.3935866 -2.4761078 -2.5576274
Tsc22d1 -1.1912274 -1.1743904 -1.1575144 -1.1405758 -1.1235514 -1.1064175 -1.0891506 -1.0717269 -1.0541227 -1.0363141 -1.0182772 -0.9999877 -0.9814216 -0.9625546 -0.9433622 -0.9238200 -0.9039034 -0.8835876 -0.8628477 -0.8416588 -0.8199973 -0.7978720 -0.7753254 -0.7524012 -0.7291436 -0.7055968 -0.6818053 -0.6578140 -0.6336677 -0.6094115 -0.5850910 -0.5607516 -0.5364394 -0.5122003 -0.4880806 -0.4641269 -0.4403859 -0.4169046 -0.3937300 -0.3709097 -0.3484910 -0.3265217 -0.3050497 -0.2841230 -0.2637897 -0.2440983 -0.2250970 -0.2068344 -0.1893591 -0.1727198 -0.1569651 -0.1421438 -0.1283046 -0.1154962 -0.1037674 -0.0931667 -0.0837426 -0.0755436 -0.0686180 -0.0630138 -0.0587790 -0.0559613 -0.0546081 -0.0547666 -0.0564836 -0.0598056 -0.0647787 -0.0714485 -0.0798602 -0.0900586 -0.1020878 -0.1159914 -0.1318123 -0.1495927 -0.1693743 -0.1911666 -0.2148953 -0.2404722 -0.2678087 -0.2968163 -0.3274065 -0.3594909 -0.3929811 -0.4277890 -0.4638266 -0.5010064 -0.5392411 -0.5784439 -0.6185283 -0.6594085 -0.7009990 -0.7432151 -0.7859725 -0.8291876 -0.8727774 -0.9166598 -0.9607532 -1.0049767 -1.0492502 -1.0934944 -1.6971413 -1.5557266 -1.4133499 -1.2702596 -1.1267121 -0.9829714 -0.8393089 -0.6960030 -0.5533390 -0.4116088 -0.2711101 -0.1321468 0.0049722 0.1399330 0.2724171 0.4021021 0.5286620 0.6517679 0.7710880 0.8862889 0.9970352 1.1029910 1.2038196 1.2991845 1.3887500 1.4721816 1.5491911 1.6197630 1.6839887 1.7419665 1.7938008 1.8396018 1.8794851 1.9135712 1.9419852 1.9648567 1.9823190 1.9945090 2.0015672 2.0036367 2.0008637 1.9933969 1.9813871 1.9649872 1.9443519 1.9196373 1.8910012 1.8586022 1.8226002 1.7831556 1.7404294 1.6945834 1.6457791 1.5941786 1.5399437 1.4832359 1.4242166 1.3630465 1.2998858 1.2348939 1.1682294 1.1000499 1.0305118 0.9597704 0.8879797 0.8152924 0.7418597 0.6678311 0.5933546 0.5185767 0.4436419 0.3686932 0.2938715 0.2193160 0.1451642 0.0715514 -0.0013886 -0.0735243 -0.1447256 -0.2148646 -0.2838190 -0.3515571 -0.4181362 -0.4836166 -0.5480576 -0.6115181 -0.6740562 -0.7357292 -0.7965938 -0.8567061 -0.9161213 -0.9748941 -1.0330786 -1.0907282 -1.1478957 -1.2046331 -1.2609921 -1.3170233 -1.3727772 -1.4283034
Maz 2.7686217 2.4656152 2.1720712 1.8885283 1.6154371 1.3531663 1.1020100 0.8621943 0.6338850 0.4171947 0.2121906 0.0189018 -0.1626736 -0.3325608 -0.4908020 -0.6374485 -0.7725550 -0.8961723 -1.0083411 -1.1090857 -1.1984240 -1.2767294 -1.3447032 -1.4029930 -1.4521834 -1.4928021 -1.5253268 -1.5501908 -1.5677878 -1.5784770 -1.5825870 -1.5804202 -1.5722558 -1.5583537 -1.5389573 -1.5142964 -1.4845900 -1.4500487 -1.4108774 -1.3672770 -1.3194471 -1.2675879 -1.2119017 -1.1525954 -1.0898819 -1.0239815 -0.9551242 -0.8835501 -0.8095118 -0.7332747 -0.6551189 -0.5753395 -0.4942479 -0.4121720 -0.3294573 -0.2464667 -0.1635808 -0.0811977 0.0002670 0.0803811 0.1586963 0.2347494 0.3080636 0.3781500 0.4445095 0.5066345 0.5640122 0.6161262 0.6624602 0.7025007 0.7357409 0.7616839 0.7798468 0.7897650 0.7909966 0.7833132 0.7670165 0.7425164 0.7102442 0.6706490 0.6241938 0.5713518 0.5126035 0.4484330 0.3793253 0.3057637 0.2282267 0.1471862 0.0631051 -0.0235643 -0.1123824 -0.2029231 -0.2947754 -0.3875444 -0.4808517 -0.5743363 -0.6676548 -0.7604816 -0.8525089 -0.9434465 -1.1225758 -0.9995456 -0.8742022 -0.7468282 -0.6177323 -0.4872498 -0.3557431 -0.2236020 -0.0912438 0.0408869 0.1723187 0.3025543 0.4310709 0.5573223 0.6807399 0.8007350 0.9167009 1.0280156 1.1340445 1.2341439 1.3276646 1.4139554 1.4923676 1.5622593 1.6230000 1.6739757 1.7146809 1.7451636 1.7657054 1.7766244 1.7782709 1.7710238 1.7552867 1.7314846 1.7000601 1.6614702 1.6161828 1.5646739 1.5074244 1.4449177 1.3776365 1.3060612 1.2306671 1.1519230 1.0702887 0.9862143 0.9001383 0.8124863 0.7236708 0.6340897 0.5441260 0.4541474 0.3645062 0.2755390 0.1875670 0.1008963 0.0158178 -0.0673915 -0.1484685 -0.2271631 -0.3032371 -0.3764635 -0.4466255 -0.5135151 -0.5769322 -0.6366831 -0.6925790 -0.7444352 -0.7920690 -0.8352981 -0.8739394 -0.9078071 -0.9367105 -0.9604526 -0.9788278 -0.9916199 -0.9985997 -0.9995228 -0.9941266 -0.9821282 -0.9632340 -0.9374263 -0.9049666 -0.8661141 -0.8211166 -0.7702137 -0.7136399 -0.6516275 -0.5844097 -0.5122229 -0.4353097 -0.3539207 -0.2683177 -0.1787750 -0.0855823 0.0109540 0.1105089 0.2127370 0.3172711 0.4237211
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Zfp235 0.0334436 -0.0124711 -0.0573086 -0.1009348 -0.1432278 -0.1840765 -0.2233802 -0.2610471 -0.2969938 -0.3311438 -0.3634267 -0.3937771 -0.4221332 -0.4484363 -0.4726287 -0.4946537 -0.5144532 -0.5319676 -0.5471334 -0.5598830 -0.5701470 -0.5779540 -0.5834279 -0.5866862 -0.5878364 -0.5869776 -0.5842017 -0.5795942 -0.5732354 -0.5652017 -0.5555656 -0.5443974 -0.5317657 -0.5177377 -0.5023807 -0.4857619 -0.4679499 -0.4490143 -0.4290273 -0.4080636 -0.3862009 -0.3635206 -0.3401083 -0.3160540 -0.2914524 -0.2664035 -0.2410126 -0.2153908 -0.1896548 -0.1639273 -0.1383367 -0.1130175 -0.0881097 -0.0637588 -0.0401155 -0.0173352 0.0044223 0.0249937 0.0442130 0.0619117 0.0779206 0.0920700 0.1041915 0.1141189 0.1216896 0.1267460 0.1291371 0.1287197 0.1253603 0.1189367 0.1093394 0.0964733 0.0802592 0.0606355 0.0375593 0.0110747 -0.0185802 -0.0511311 -0.0863004 -0.1238100 -0.1633838 -0.2047499 -0.2476425 -0.2918037 -0.3369854 -0.3829500 -0.4294718 -0.4763377 -0.5233482 -0.5703173 -0.6170728 -0.6634568 -0.7093253 -0.7545479 -0.7990078 -0.8426008 -0.8852355 -0.9268321 -0.9673222 -1.0066475 -1.3868231 -1.3062221 -1.2181854 -1.1222964 -1.0181740 -0.9054872 -0.7839722 -0.6534508 -0.5138508 -0.3652267 -0.2077820 -0.0418904 0.1318831 0.3127635 0.4997491 0.6915998 0.8868295 1.0837053 1.2802535 1.4742739 1.6633626 1.8449445 2.0163145 2.1746875 2.3172577 2.4412638 2.5442606 2.6252298 2.6839406 2.7205059 2.7353579 2.7292196 2.7030707 2.6581106 2.5957196 2.5174196 2.4248350 2.3196552 2.2035995 2.0783852 1.9456982 1.8071685 1.6643489 1.5186983 1.3715684 1.2241945 1.0776898 0.9330430 0.7911183 0.6526585 0.5182895 0.3885269 0.2637837 0.1443786 0.0305454 -0.0775576 -0.1798387 -0.2762627 -0.3668425 -0.4516308 -0.5307113 -0.6041923 -0.6721990 -0.7348680 -0.7923409 -0.8447599 -0.8922624 -0.9349772 -0.9730202 -1.0064906 -1.0354670 -1.0600043 -1.0801290 -1.0958357 -1.1070820 -1.1137840 -1.1158094 -1.1129712 -1.1050187 -1.0916272 -1.0723968 -1.0470813 -1.0156026 -0.9778275 -0.9335638 -0.8825647 -0.8245340 -0.7591309 -0.6859745 -0.6046500 -0.5147144 -0.4157045 -0.3071448 -0.1885588 -0.0594801 0.0805328 0.2318806 0.3949048 0.5698668 0.7569254
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Rxrg 0.3279448 0.3208844 0.3139306 0.3071670 0.3006763 0.2945401 0.2888395 0.2836548 0.2790657 0.2751521 0.2719934 0.2696694 0.2682606 0.2678481 0.2685144 0.2703435 0.2734215 0.2778370 0.2836815 0.2910500 0.3000380 0.3106533 0.3228145 0.3364368 0.3514359 0.3677271 0.3852247 0.4038418 0.4234892 0.4440755 0.4655067 0.4876852 0.5105101 0.5338767 0.5576763 0.5817958 0.6061177 0.6305202 0.6548770 0.6790570 0.7029252 0.7263420 0.7491638 0.7712435 0.7924305 0.8125711 0.8315093 0.8490872 0.8651455 0.8795246 0.8920648 0.9026076 0.9109966 0.9170782 0.9207027 0.9217257 0.9200089 0.9154214 0.9078408 0.8971548 0.8832622 0.8660741 0.8455155 0.8215265 0.7940634 0.7630998 0.7286284 0.6906614 0.6492317 0.6043938 0.5562248 0.5048242 0.4503150 0.3928436 0.3325796 0.2697808 0.2048898 0.1383674 0.0706585 0.0021879 -0.0666420 -0.1354541 -0.2038987 -0.2716548 -0.3384313 -0.4039680 -0.4680350 -0.5304330 -0.5909925 -0.6495729 -0.7060608 -0.7603693 -0.8124353 -0.8622186 -0.9096990 -0.9548751 -0.9977618 -1.0383883 -1.0767962 -1.1130379 -1.3845221 -1.3368761 -1.2818962 -1.2187209 -1.1464738 -1.0642926 -0.9713645 -0.8669699 -0.7505322 -0.6216727 -0.4802688 -0.3265100 -0.1609502 0.0154495 0.2012910 0.3947263 0.5934636 0.7947935 0.9956351 1.1925994 1.3820683 1.5602844 1.7234481 1.8678196 1.9898210 2.0861389 2.1540807 2.1929878 2.2033415 2.1861420 2.1428438 2.0752884 1.9856371 1.8763029 1.7498837 1.6090952 1.4567061 1.2954759 1.1280958 0.9571347 0.7849914 0.6138544 0.4456703 0.2821219 0.1246159 -0.0257193 -0.1680271 -0.3017079 -0.4263982 -0.5419445 -0.6483744 -0.7458665 -0.8347205 -0.9153282 -0.9881473 -1.0536783 -1.1124444 -1.1649750 -1.2117919 -1.2533996 -1.2902774 -1.3228741 -1.3516046 -1.3768481 -1.3989474 -1.4182091 -1.4349042 -1.4492693 -1.4615079 -1.4717912 -1.4802592 -1.4870214 -1.4921568 -1.4957129 -1.4977051 -1.4981131 -1.4968779 -1.4938954 -1.4890092 -1.4819987 -1.4725692 -1.4604255 -1.4452789 -1.4267601 -1.4044078 -1.3776573 -1.3458287 -1.3081120 -1.2635523 -1.2110335 -1.1492635 -1.0767613 -0.9918484 -0.8926470 -0.7770889 -0.6429379 -0.4878296 -0.3093335 -0.1050380 0.1273385
Id3 -0.8947749 -0.8435085 -0.7917539 -0.7395898 -0.6870978 -0.6343625 -0.5814713 -0.5285139 -0.4755826 -0.4227719 -0.3701784 -0.3179007 -0.2660388 -0.2146948 -0.1639715 -0.1139736 -0.0648063 -0.0165759 0.0306106 0.0766457 0.1214233 0.1648787 0.2069897 0.2477376 0.2871053 0.3250770 0.3616386 0.3967769 0.4304802 0.4627382 0.4935415 0.5228817 0.5507518 0.5771456 0.6020579 0.6254844 0.6474217 0.6678672 0.6868192 0.7042768 0.7202396 0.7347083 0.7476839 0.7591684 0.7691642 0.7776744 0.7847028 0.7902537 0.7943320 0.7969431 0.7980930 0.7977883 0.7960359 0.7928435 0.7882192 0.7821714 0.7747094 0.7658427 0.7555814 0.7439361 0.7309178 0.7165381 0.7008092 0.6837435 0.6653542 0.6456549 0.6246597 0.6023833 0.5788409 0.5540481 0.5280214 0.5007776 0.4723342 0.4427091 0.4119211 0.3799997 0.3470028 0.3129927 0.2780318 0.2421822 0.2055063 0.1680659 0.1299227 0.0911382 0.0517733 0.0118887 -0.0284555 -0.0691998 -0.1102852 -0.1516534 -0.1932469 -0.2350088 -0.2768833 -0.3188154 -0.3607510 -0.4026372 -0.4444219 -0.4860543 -0.5274849 -0.5686651 -1.1945080 -1.0668817 -0.9355052 -0.8008625 -0.6634846 -0.5239437 -0.3828472 -0.2408320 -0.0985582 0.0432965 0.1840421 0.3229815 0.4594145 0.5926419 0.7219683 0.8467051 0.9661727 1.0797018 1.1866351 1.2863282 1.3781503 1.4614853 1.5357317 1.6003037 1.6546316 1.6981625 1.7304531 1.7516344 1.7620658 1.7621268 1.7522139 1.7327386 1.7041253 1.6668106 1.6212414 1.5678740 1.5071733 1.4396121 1.3656695 1.2858312 1.2005878 1.1104342 1.0158688 0.9173921 0.8155059 0.7107116 0.6035093 0.4943953 0.3838613 0.2723917 0.1604621 0.0485367 -0.0629336 -0.1735136 -0.2827862 -0.3903543 -0.4958430 -0.5989014 -0.6992041 -0.7964525 -0.8903756 -0.9807304 -1.0673017 -1.1499018 -1.2283690 -1.3025667 -1.3723809 -1.4377177 -1.4985010 -1.5546688 -1.6061701 -1.6529609 -1.6950008 -1.7322483 -1.7646573 -1.7921723 -1.8147240 -1.8322253 -1.8445657 -1.8516076 -1.8531909 -1.8493611 -1.8403670 -1.8264362 -1.8077707 -1.7845529 -1.7569514 -1.7251261 -1.6892333 -1.6494306 -1.6058811 -1.5587573 -1.5082451 -1.4545469 -1.3978842 -1.3385005 -1.2766626 -1.2126624 -1.1468176 -1.0794719
Zfp931 -0.3954399 -0.3373900 -0.2784260 -0.2186595 -0.1582108 -0.0972087 -0.0357910 0.0258957 0.0876957 0.1494446 0.2109689 0.2720866 0.3326073 0.3923322 0.4510552 0.5085627 0.5646344 0.6190442 0.6715606 0.7219475 0.7699698 0.8154893 0.8584712 0.8988913 0.9367317 0.9719807 1.0046323 1.0346866 1.0621492 1.0870311 1.1093484 1.1291226 1.1463797 1.1611504 1.1734696 1.1833765 1.1909142 1.1961293 1.1990719 1.1997951 1.1983551 1.1948108 1.1892233 1.1816562 1.1721749 1.1608466 1.1477401 1.1329253 1.1164736 1.0984570 1.0789482 1.0580206 1.0357478 1.0122036 0.9874618 0.9615962 0.9346800 0.9067860 0.8779867 0.8483536 0.8179573 0.7868679 0.7551540 0.7228832 0.6901221 0.6569357 0.6233879 0.5895410 0.5554561 0.5211925 0.4868081 0.4523592 0.4179007 0.3834856 0.3491655 0.3149802 0.2809417 0.2470571 0.2133334 0.1797773 0.1463954 0.1131939 0.0801789 0.0473563 0.0147319 -0.0176889 -0.0499009 -0.0818989 -0.1136781 -0.1452338 -0.1765614 -0.2076567 -0.2385157 -0.2691342 -0.2995087 -0.3296355 -0.3595112 -0.3891326 -0.4184967 -0.4476005 -0.8840425 -0.7899371 -0.6928822 -0.5931560 -0.4910829 -0.3870361 -0.2814392 -0.1747675 -0.0675488 0.0396372 0.1461594 0.2513378 0.3544457 0.4547140 0.5513360 0.6434735 0.7302633 0.8108260 0.8842744 0.9497241 1.0063037 1.0531672 1.0895058 1.1145607 1.1276370 1.1281164 1.1155888 1.0904534 1.0534610 1.0054329 0.9472456 0.8798155 0.8040857 0.7210123 0.6315525 0.5366530 0.4372403 0.3342114 0.2284267 0.1207031 0.0118089 -0.0975401 -0.2066835 -0.3150177 -0.4219974 -0.5271345 -0.6299976 -0.7302101 -0.8274478 -0.9214359 -1.0119459 -1.0987917 -1.1818262 -1.2609366 -1.3360411 -1.4070844 -1.4740339 -1.5368757 -1.5956108 -1.6502513 -1.7008172 -1.7473328 -1.7898232 -1.8283119 -1.8628166 -1.8933474 -1.9199026 -1.9424665 -1.9610060 -1.9754667 -1.9857700 -1.9918088 -1.9934429 -1.9904944 -1.9827415 -1.9699121 -1.9516760 -1.9276358 -1.8973162 -1.8601508 -1.8154797 -1.7627990 -1.7017891 -1.6320759 -1.5532245 -1.4647440 -1.3660921 -1.2566816 -1.1358869 -1.0030525 -0.8575029 -0.6985540 -0.5255271 -0.3377647 -0.1346485 0.0843800 0.3197972 0.5719729 0.8411447 1.1273911
Foxn2 0.2349836 0.2656179 0.2964265 0.3273679 0.3583999 0.3894789 0.4205600 0.4515973 0.4825437 0.5133510 0.5439695 0.5743488 0.6044372 0.6341819 0.6635290 0.6924238 0.7208103 0.7486321 0.7758314 0.8023501 0.8281295 0.8531240 0.8773012 0.9006290 0.9230758 0.9446099 0.9651997 0.9848139 1.0034217 1.0209922 1.0374951 1.0529005 1.0671790 1.0803014 1.0922396 1.1029656 1.1124523 1.1206735 1.1276034 1.1332173 1.1374912 1.1404022 1.1419284 1.1420487 1.1407434 1.1379937 1.1337822 1.1280927 1.1209101 1.1122210 1.1020130 1.0902756 1.0769993 1.0621766 1.0458012 1.0278686 1.0083760 0.9873221 0.9647074 0.9405343 0.9148068 0.8875307 0.8587137 0.8283653 0.7964970 0.7631219 0.7282552 0.6919140 0.6541171 0.6148853 0.5742414 0.5322097 0.4888169 0.4440910 0.3980621 0.3507830 0.3023622 0.2529155 0.2025565 0.1513962 0.0995426 0.0471011 -0.0058263 -0.0591406 -0.1127465 -0.1665518 -0.2204680 -0.2744102 -0.3282972 -0.3820511 -0.4355981 -0.4888678 -0.5417935 -0.5943119 -0.6463636 -0.6978923 -0.7488454 -0.7991733 -0.8488301 -0.8977726 -1.2605748 -1.1608666 -1.0578451 -0.9517361 -0.8428092 -0.7313803 -0.6178145 -0.5025277 -0.3859890 -0.2687214 -0.1513018 -0.0343616 0.0814157 0.1952959 0.3064977 0.4141973 0.5175333 0.6156141 0.7075252 0.7923387 0.8691231 0.9369546 0.9949294 1.0421766 1.0778716 1.1012507 1.1117383 1.1095337 1.0951831 1.0693133 1.0326181 0.9858460 0.9297874 0.8652625 0.7931102 0.7141769 0.6293071 0.5393344 0.4450734 0.3473130 0.2468104 0.1442865 0.0404221 -0.0641455 -0.1688237 -0.2730663 -0.3763736 -0.4782924 -0.5784145 -0.6763761 -0.7718553 -0.8645699 -0.9542754 -1.0407616 -1.1238501 -1.2033910 -1.2792601 -1.3513555 -1.4195945 -1.4839106 -1.5442504 -1.6005705 -1.6528346 -1.7010108 -1.7450683 -1.7849748 -1.8206938 -1.8521816 -1.8793842 -1.9022348 -1.9206501 -1.9345273 -1.9437404 -1.9481363 -1.9475304 -1.9417015 -1.9303867 -1.9132747 -1.8899987 -1.8601278 -1.8231697 -1.7788311 -1.7270366 -1.6676798 -1.6006168 -1.5256718 -1.4426423 -1.3513047 -1.2514198 -1.1427395 -1.0250132 -0.8979952 -0.7614529 -0.6151757 -0.4589844 -0.2927419 -0.1163642 0.0701672 0.2667930 0.4733629
Id2 -0.4809608 -0.4241324 -0.3668450 -0.3091999 -0.2513024 -0.1932607 -0.1351865 -0.0771944 -0.0194018 0.0380711 0.0951017 0.1515652 0.2073344 0.2622808 0.3162738 0.3691816 0.4208711 0.4712084 0.5200585 0.5672861 0.6127580 0.6563998 0.6981975 0.7381419 0.7762260 0.8124443 0.8467934 0.8792714 0.9098783 0.9386154 0.9654854 0.9904927 1.0136427 1.0349423 1.0543994 1.0720232 1.0878238 1.1018125 1.1140015 1.1244040 1.1330340 1.1399063 1.1450368 1.1484420 1.1501391 1.1501462 1.1484819 1.1451656 1.1402173 1.1336578 1.1255082 1.1157905 1.1045270 1.0917408 1.0774553 1.0616946 1.0444832 1.0258463 1.0058093 0.9843983 0.9616397 0.9375605 0.9121881 0.8855503 0.8576754 0.8285919 0.7983291 0.7669164 0.7343836 0.7007611 0.6660794 0.6303696 0.5936631 0.5559915 0.5173870 0.4778878 0.4375487 0.3964266 0.3545785 0.3120609 0.2689303 0.2252425 0.1810531 0.1364173 0.0913896 0.0460240 0.0003740 -0.0455079 -0.0915695 -0.1377597 -0.1840281 -0.2303252 -0.2766025 -0.3228124 -0.3689083 -0.4148447 -0.4605772 -0.5060627 -0.5512590 -0.5961254 -0.9890735 -0.8859668 -0.7808000 -0.6739335 -0.5657556 -0.4566804 -0.3471459 -0.2376112 -0.1285546 -0.0204705 0.0861330 0.1907366 0.2928124 0.3918265 0.4872410 0.5785165 0.6651141 0.7464971 0.8221335 0.8914968 0.9540688 1.0093402 1.0568132 1.0960025 1.1264374 1.1476639 1.1593269 1.1615787 1.1547746 1.1392902 1.1155180 1.0838656 1.0447540 0.9986151 0.9458910 0.8870315 0.8224935 0.7527390 0.6782334 0.5994450 0.5168423 0.4308933 0.3420635 0.2508143 0.1576013 0.0628724 -0.0329336 -0.1293891 -0.2260797 -0.3226053 -0.4185824 -0.5136451 -0.6074470 -0.6996619 -0.7899853 -0.8781348 -0.9638506 -1.0468960 -1.1270567 -1.2041410 -1.2779786 -1.3484197 -1.4153335 -1.4786067 -1.5381416 -1.5938539 -1.6456704 -1.6935265 -1.7373635 -1.7771261 -1.8127589 -1.8442041 -1.8713979 -1.8942674 -1.9127275 -1.9266772 -1.9359964 -1.9405417 -1.9401429 -1.9345986 -1.9236824 -1.9073605 -1.8857966 -1.8591404 -1.8275230 -1.7910627 -1.7498703 -1.7040541 -1.6537246 -1.5989992 -1.5400066 -1.4768906 -1.4098139 -1.3389614 -1.2645429 -1.1867960 -1.1059875 -1.0224151 -0.9364081 -0.8483278 
heatmap_matrix_ori_q_value_5_10_minus_5 <- left_join(select(transcription_factors_table_q_value_5_10_minus_5, gene, pval, qval, num_cells_expressed), heatmap_matrix_ori_q_value_5_10_minus_5)
write.table(heatmap_matrix_ori_q_value_5_10_minus_5, file = file.path(tables_directory, "5.1-significant_transcription_factors_beam_analysis_qval_5_10_minus_5_plot_genes_branched_heatmap_matrix_ori.txt"), sep="\t", quote=FALSE, row.names=FALSE)

2.2 q value < 0.01 (plot_genes_branched_heatmap)

significant_genes_q_value_0.01 <- filter(beam_results, qval < 0.01) %>% .$gene 
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes:  6623
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 375
plot_genes_branched_heatmap(monocle[significant_transcription_factors_q_value_0.01,], branch_labels=c("Ependymal cells", "Astrocytes"), cluster_rows=TRUE, num_clusters=6, show_rownames = TRUE)

## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
plot_genes_branched_heatmap_output_q_value_0.01 <- plot_genes_branched_heatmap(monocle[significant_transcription_factors_q_value_0.01,], branch_labels=c("Ependymal cells", "Astrocytes"), cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_branched_heatmap_output_q_value_0.01[["ph_res"]], file.path("figures", "5.1-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_beam_analysis", "beam_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=36)
## pdf 
##   2
heatmap_matrix_ori_q_value_0.01 <- plot_genes_branched_heatmap_output_q_value_0.01[["heatmap_matrix_ori"]]
ph_res_q_value_0.01 <- plot_genes_branched_heatmap_output_q_value_0.01[["ph_res"]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_ori_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])

transcription_factors_table_q_value_0.01 <- filter(beam_results, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))

write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "5.1-significant_transcription_factors_beam_analysis_qval_0.01_plot_genes_branched_heatmap.txt"), sep="\t", quote=FALSE, row.names=FALSE)

heatmap_matrix_ori_q_value_0.01 <- plot_genes_branched_heatmap_output_q_value_0.01[["heatmap_matrix_ori"]]
heatmap_matrix_ori_q_value_0.01 <- as.data.frame(heatmap_matrix_ori_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_ori_q_value_0.01 <- heatmap_matrix_ori_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_ori_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
gene 100 99 98 97 96 95 94 93 92 91 90 89 88 87 86 85 84 83 82 81 80 79 78 77 76 75 74 73 72 71 70 69 68 67 66 65 64 63 62 61 60 59 58 57 56 55 54 53 52 51 50 49 48 47 46 45 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200
Tbx1 3.0000000 3.0000000 3.0000000 3.0000000 2.3519464 1.6284311 1.1105744 0.7393728 0.4725912 0.2801544 0.1407162 0.0391522 -0.0352491 -0.0900791 -0.1307262 -0.1610228 -0.1837013 -0.2007135 -0.2134546 -0.2229194 -0.2298139 -0.2346918 -0.2379866 -0.2399901 -0.2408918 -0.2408057 -0.2397882 -0.2378486 -0.2349552 -0.2310389 -0.2259939 -0.2196768 -0.2119051 -0.2024546 -0.1910569 -0.1773973 -0.1611139 -0.1417988 -0.1190030 -0.0922454 -0.0610289 -0.0248640 0.0166972 0.0640173 0.1173173 0.1766105 0.2416286 0.3117451 0.3859030 0.4625585 0.5396522 0.6146217 0.6844681 0.7458855 0.7954566 0.8299061 0.8463958 0.8428307 0.8181380 0.7724764 0.7073347 0.6254908 0.5308207 0.4279706 0.3219303 0.2175661 0.1191799 0.0301586 -0.0472379 -0.1119312 -0.1639283 -0.2041105 -0.2339567 -0.2552550 -0.2698481 -0.2794334 -0.2854557 -0.2890822 -0.2911803 -0.2923493 -0.2929779 -0.2933046 -0.2934692 -0.2935496 -0.2935878 -0.2936055 -0.2936135 -0.2936171 -0.2936186 -0.2936192 -0.2936195 -0.2936196 -0.2936197 -0.2936197 -0.2936197 -0.2936197 -0.2936197 -0.2936197 -0.2936197 -0.2936197 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485 -0.2930485
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Grhl3 3.0000000 3.0000000 3.0000000 1.5780227 0.7258175 0.2880315 0.0636731 -0.0515956 -0.1111582 -0.1421859 -0.1585110 -0.1672006 -0.1718867 -0.1744507 -0.1758757 -0.1766812 -0.1771447 -0.1774166 -0.1775792 -0.1776784 -0.1777402 -0.1777796 -0.1778054 -0.1778226 -0.1778344 -0.1778426 -0.1778485 -0.1778526 -0.1778557 -0.1778579 -0.1778595 -0.1778607 -0.1778614 -0.1778619 -0.1778622 -0.1778622 -0.1778619 -0.1778615 -0.1778608 -0.1778598 -0.1778585 -0.1778568 -0.1778547 -0.1778520 -0.1778485 -0.1778442 -0.1778386 -0.1778316 -0.1778227 -0.1778112 -0.1777965 -0.1777775 -0.1777530 -0.1777212 -0.1776799 -0.1776262 -0.1775563 -0.1774652 -0.1773464 -0.1771917 -0.1769904 -0.1767292 -0.1763909 -0.1759545 -0.1753939 -0.1746775 -0.1737673 -0.1726189 -0.1711812 -0.1693966 -0.1672031 -0.1645355 -0.1613298 -0.1575274 -0.1530815 -0.1479568 -0.1421127 -0.1355129 -0.1281285 -0.1199385 -0.1109303 -0.1010988 -0.0904464 -0.0789813 -0.0667165 -0.0536677 -0.0398516 -0.0252832 -0.0099741 0.0060707 0.0228549 0.0403935 0.0587158 0.0778677 0.0979145 0.1189443 0.1410709 0.1644375 0.1892209 0.2156364 0.2829469 0.2339537 0.1902312 0.1512822 0.1166405 0.0858722 0.0585768 0.0343874 0.0129692 -0.0059813 -0.0227377 -0.0375461 -0.0506267 -0.0621758 -0.0723679 -0.0813579 -0.0892822 -0.0962615 -0.1024015 -0.1077950 -0.1125227 -0.1166551 -0.1202531 -0.1233689 -0.1260470 -0.1283251 -0.1302379 -0.1318351 -0.1331662 -0.1342728 -0.1351912 -0.1359528 -0.1365860 -0.1371163 -0.1375674 -0.1379617 -0.1383204 -0.1386636 -0.1390111 -0.1393818 -0.1397938 -0.1402643 -0.1408094 -0.1414439 -0.1421803 -0.1430295 -0.1439993 -0.1450948 -0.1463176 -0.1476654 -0.1491326 -0.1507091 -0.1523814 -0.1541324 -0.1559419 -0.1577872 -0.1596440 -0.1614873 -0.1632922 -0.1650351 -0.1666944 -0.1682514 -0.1696910 -0.1710022 -0.1721783 -0.1732167 -0.1741189 -0.1748902 -0.1755384 -0.1760740 -0.1765088 -0.1768556 -0.1771271 -0.1773357 -0.1774929 -0.1776091 -0.1776934 -0.1777531 -0.1777947 -0.1778229 -0.1778418 -0.1778540 -0.1778618 -0.1778666 -0.1778695 -0.1778713 -0.1778723 -0.1778729 -0.1778732 -0.1778734 -0.1778735 -0.1778736 -0.1778736 -0.1778736 -0.1778736 -0.1778736 -0.1778736 -0.1778736 -0.1778736 -0.1778736
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Prrx2 -0.5270924 -0.5432961 -0.5591853 -0.5746522 -0.5895943 -0.6039139 -0.6175177 -0.6303164 -0.6422238 -0.6531563 -0.6630322 -0.6717705 -0.6792906 -0.6855109 -0.6903479 -0.6937152 -0.6955222 -0.6956729 -0.6940643 -0.6905853 -0.6851185 -0.6776346 -0.6681947 -0.6568575 -0.6436760 -0.6286993 -0.6119736 -0.5935432 -0.5734519 -0.5517439 -0.5284652 -0.5036644 -0.4773938 -0.4497105 -0.4206773 -0.3903639 -0.3588478 -0.3262151 -0.2925613 -0.2579926 -0.2226263 -0.1865914 -0.1500293 -0.1130944 -0.0759542 -0.0387897 -0.0017952 0.0348220 0.0708417 0.1060314 0.1401475 0.1729363 0.2041350 0.2334739 0.2606781 0.2854694 0.3075693 0.3267010 0.3425931 0.3549822 0.3636164 0.3682588 0.3686910 0.3647168 0.3561660 0.3428974 0.3248029 0.3018105 0.2738869 0.2410408 0.2033245 0.1608356 0.1137186 0.0621643 0.0064107 -0.0531681 -0.1159310 -0.1812084 -0.2483535 -0.3167503 -0.3858200 -0.4550258 -0.5238774 -0.5919327 -0.6588002 -0.7241385 -0.7876562 -0.8491105 -0.9083047 -0.9650859 -1.0193417 -1.0709968 -1.1200093 -1.1663670 -1.2100839 -1.2511963 -1.2897592 -1.3258437 -1.3595328 -1.3909198 -1.5560925 -1.5195933 -1.4778163 -1.4301277 -1.3758563 -1.3143024 -1.2447501 -1.1664840 -1.0788095 -0.9810783 -0.8727181 -0.7532667 -0.6224088 -0.4800166 -0.3261896 -0.1612950 0.0139961 0.1986776 0.3913855 0.5903855 0.7935726 0.9984848 1.2023317 1.4020380 1.5943012 1.7756634 1.9427735 2.0934546 2.2262317 2.3399734 2.4338942 2.5075479 2.5608140 2.5938774 2.6072027 2.6015058 2.5777215 2.5369712 2.4805285 2.4097858 2.3262212 2.2313674 2.1267817 2.0140191 1.8946073 1.7700257 1.6416861 1.5109176 1.3789548 1.2469281 1.1158586 0.9866542 0.8601100 0.7369091 0.6176276 0.5027393 0.3926225 0.2875687 0.1877901 0.0934292 0.0045676 -0.0787652 -0.1565823 -0.2289317 -0.2958880 -0.3575449 -0.4140084 -0.4653901 -0.5118016 -0.5533484 -0.5901253 -0.6222108 -0.6496627 -0.6725129 -0.6907622 -0.7043755 -0.7132747 -0.7173330 -0.7163662 -0.7101236 -0.6982880 -0.6807117 -0.6574252 -0.6284073 -0.5935820 -0.5528251 -0.5059711 -0.4528191 -0.3931395 -0.3266802 -0.2531746 -0.1723493 -0.0839330 0.0123327 0.1166827 0.2293148 0.3503767 0.4799505 0.6180368 0.7645375
Tsc22d1 -1.1912274 -1.1743904 -1.1575144 -1.1405758 -1.1235514 -1.1064175 -1.0891506 -1.0717269 -1.0541227 -1.0363141 -1.0182772 -0.9999877 -0.9814216 -0.9625546 -0.9433622 -0.9238200 -0.9039034 -0.8835876 -0.8628477 -0.8416588 -0.8199973 -0.7978720 -0.7753254 -0.7524012 -0.7291436 -0.7055968 -0.6818053 -0.6578140 -0.6336677 -0.6094115 -0.5850910 -0.5607516 -0.5364394 -0.5122003 -0.4880806 -0.4641269 -0.4403859 -0.4169046 -0.3937300 -0.3709097 -0.3484910 -0.3265217 -0.3050497 -0.2841230 -0.2637897 -0.2440983 -0.2250970 -0.2068344 -0.1893591 -0.1727198 -0.1569651 -0.1421438 -0.1283046 -0.1154962 -0.1037674 -0.0931667 -0.0837426 -0.0755436 -0.0686180 -0.0630138 -0.0587790 -0.0559613 -0.0546081 -0.0547666 -0.0564836 -0.0598056 -0.0647787 -0.0714485 -0.0798602 -0.0900586 -0.1020878 -0.1159914 -0.1318123 -0.1495927 -0.1693743 -0.1911666 -0.2148953 -0.2404722 -0.2678087 -0.2968163 -0.3274065 -0.3594909 -0.3929811 -0.4277890 -0.4638266 -0.5010064 -0.5392411 -0.5784439 -0.6185283 -0.6594085 -0.7009990 -0.7432151 -0.7859725 -0.8291876 -0.8727774 -0.9166598 -0.9607532 -1.0049767 -1.0492502 -1.0934944 -1.6971413 -1.5557266 -1.4133499 -1.2702596 -1.1267121 -0.9829714 -0.8393089 -0.6960030 -0.5533390 -0.4116088 -0.2711101 -0.1321468 0.0049722 0.1399330 0.2724171 0.4021021 0.5286620 0.6517679 0.7710880 0.8862889 0.9970352 1.1029910 1.2038196 1.2991845 1.3887500 1.4721816 1.5491911 1.6197630 1.6839887 1.7419665 1.7938008 1.8396018 1.8794851 1.9135712 1.9419852 1.9648567 1.9823190 1.9945090 2.0015672 2.0036367 2.0008637 1.9933969 1.9813871 1.9649872 1.9443519 1.9196373 1.8910012 1.8586022 1.8226002 1.7831556 1.7404294 1.6945834 1.6457791 1.5941786 1.5399437 1.4832359 1.4242166 1.3630465 1.2998858 1.2348939 1.1682294 1.1000499 1.0305118 0.9597704 0.8879797 0.8152924 0.7418597 0.6678311 0.5933546 0.5185767 0.4436419 0.3686932 0.2938715 0.2193160 0.1451642 0.0715514 -0.0013886 -0.0735243 -0.1447256 -0.2148646 -0.2838190 -0.3515571 -0.4181362 -0.4836166 -0.5480576 -0.6115181 -0.6740562 -0.7357292 -0.7965938 -0.8567061 -0.9161213 -0.9748941 -1.0330786 -1.0907282 -1.1478957 -1.2046331 -1.2609921 -1.3170233 -1.3727772 -1.4283034
Maz 2.7686217 2.4656152 2.1720712 1.8885283 1.6154371 1.3531663 1.1020100 0.8621943 0.6338850 0.4171947 0.2121906 0.0189018 -0.1626736 -0.3325608 -0.4908020 -0.6374485 -0.7725550 -0.8961723 -1.0083411 -1.1090857 -1.1984240 -1.2767294 -1.3447032 -1.4029930 -1.4521834 -1.4928021 -1.5253268 -1.5501908 -1.5677878 -1.5784770 -1.5825870 -1.5804202 -1.5722558 -1.5583537 -1.5389573 -1.5142964 -1.4845900 -1.4500487 -1.4108774 -1.3672770 -1.3194471 -1.2675879 -1.2119017 -1.1525954 -1.0898819 -1.0239815 -0.9551242 -0.8835501 -0.8095118 -0.7332747 -0.6551189 -0.5753395 -0.4942479 -0.4121720 -0.3294573 -0.2464667 -0.1635808 -0.0811977 0.0002670 0.0803811 0.1586963 0.2347494 0.3080636 0.3781500 0.4445095 0.5066345 0.5640122 0.6161262 0.6624602 0.7025007 0.7357409 0.7616839 0.7798468 0.7897650 0.7909966 0.7833132 0.7670165 0.7425164 0.7102442 0.6706490 0.6241938 0.5713518 0.5126035 0.4484330 0.3793253 0.3057637 0.2282267 0.1471862 0.0631051 -0.0235643 -0.1123824 -0.2029231 -0.2947754 -0.3875444 -0.4808517 -0.5743363 -0.6676548 -0.7604816 -0.8525089 -0.9434465 -1.1225758 -0.9995456 -0.8742022 -0.7468282 -0.6177323 -0.4872498 -0.3557431 -0.2236020 -0.0912438 0.0408869 0.1723187 0.3025543 0.4310709 0.5573223 0.6807399 0.8007350 0.9167009 1.0280156 1.1340445 1.2341439 1.3276646 1.4139554 1.4923676 1.5622593 1.6230000 1.6739757 1.7146809 1.7451636 1.7657054 1.7766244 1.7782709 1.7710238 1.7552867 1.7314846 1.7000601 1.6614702 1.6161828 1.5646739 1.5074244 1.4449177 1.3776365 1.3060612 1.2306671 1.1519230 1.0702887 0.9862143 0.9001383 0.8124863 0.7236708 0.6340897 0.5441260 0.4541474 0.3645062 0.2755390 0.1875670 0.1008963 0.0158178 -0.0673915 -0.1484685 -0.2271631 -0.3032371 -0.3764635 -0.4466255 -0.5135151 -0.5769322 -0.6366831 -0.6925790 -0.7444352 -0.7920690 -0.8352981 -0.8739394 -0.9078071 -0.9367105 -0.9604526 -0.9788278 -0.9916199 -0.9985997 -0.9995228 -0.9941266 -0.9821282 -0.9632340 -0.9374263 -0.9049666 -0.8661141 -0.8211166 -0.7702137 -0.7136399 -0.6516275 -0.5844097 -0.5122229 -0.4353097 -0.3539207 -0.2683177 -0.1787750 -0.0855823 0.0109540 0.1105089 0.2127370 0.3172711 0.4237211 
heatmap_matrix_ori_q_value_0.01 <- left_join(select(transcription_factors_table_q_value_0.01, gene, pval, qval, num_cells_expressed), heatmap_matrix_ori_q_value_0.01)
write.table(heatmap_matrix_ori_q_value_0.01, file = file.path(tables_directory, "5.1-significant_transcription_factors_beam_analysis_qval_0.01_plot_genes_branched_heatmap_matrix_ori.txt"), sep="\t", quote=FALSE, row.names=FALSE)

2.3 Plotting of genes differentially expressed between branches

2.3.1 Top 10 differentially expressed genes

transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

3 Session info

sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
## 
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] splines   stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] viridis_0.5.1       viridisLite_0.3.0   forcats_0.4.0      
##  [4] stringr_1.4.0       dplyr_0.8.0.1       purrr_0.3.0        
##  [7] tidyr_0.8.2         tibble_2.0.1        tidyverse_1.2.1    
## [10] Seurat_2.3.4        cowplot_0.9.4       R.utils_2.8.0      
## [13] R.oo_1.22.0         R.methodsS3_1.7.1   readr_1.3.1        
## [16] readxl_1.3.0        patchwork_0.0.1     monocle_2.10.1     
## [19] DDRTree_0.1.5       irlba_2.3.3         VGAM_1.1-1         
## [22] Biobase_2.42.0      BiocGenerics_0.28.0 Matrix_1.2-15      
## [25] kableExtra_1.0.1    ggedit_0.3.0        ggplot2_3.1.0      
## [28] cytokit_0.6.0       pheatmap_1.0.12     colorRamps_2.3     
## 
## loaded via a namespace (and not attached):
##   [1] snow_0.4-3           backports_1.1.3      Hmisc_4.2-0         
##   [4] plyr_1.8.4           igraph_1.2.4         lazyeval_0.2.2      
##   [7] densityClust_0.3     fastICA_1.2-1        digest_0.6.18       
##  [10] foreach_1.4.4        htmltools_0.3.6      lars_1.2            
##  [13] gdata_2.18.0         magrittr_1.5         checkmate_1.9.1     
##  [16] cluster_2.0.7-1      mixtools_1.1.0       ROCR_1.0-7          
##  [19] limma_3.38.3         modelr_0.1.3         matrixStats_0.54.0  
##  [22] docopt_0.6.1         colorspace_1.4-0     ggrepel_0.8.0       
##  [25] rvest_0.3.2          haven_2.0.0          xfun_0.4            
##  [28] sparsesvd_0.1-4      crayon_1.3.4         jsonlite_1.6        
##  [31] survival_2.43-3      zoo_1.8-4            iterators_1.0.10    
##  [34] ape_5.2              glue_1.3.0           gtable_0.2.0        
##  [37] webshot_0.5.1        kernlab_0.9-27       prabclus_2.2-7      
##  [40] DEoptimR_1.0-8       scales_1.0.0         mvtnorm_1.0-8       
##  [43] bibtex_0.4.2         miniUI_0.1.1.1       Rcpp_1.0.0          
##  [46] metap_1.1            dtw_1.20-1           xtable_1.8-3        
##  [49] htmlTable_1.13.1     reticulate_1.11.1    foreign_0.8-71      
##  [52] bit_1.1-14           proxy_0.4-22         mclust_5.4.2        
##  [55] SDMTools_1.1-221     Formula_1.2-3        tsne_0.1-3          
##  [58] htmlwidgets_1.3      httr_1.4.0           FNN_1.1.3           
##  [61] gplots_3.0.1.1       RColorBrewer_1.1-2   shinyAce_0.3.3      
##  [64] fpc_2.1-11.1         acepack_1.4.1        modeltools_0.2-22   
##  [67] ica_1.0-2            pkgconfig_2.0.2      flexmix_2.3-14      
##  [70] nnet_7.3-12          labeling_0.3         tidyselect_0.2.5    
##  [73] rlang_0.3.1          reshape2_1.4.3       later_0.8.0         
##  [76] cellranger_1.1.0     munsell_0.5.0        tools_3.5.0         
##  [79] cli_1.0.1            generics_0.0.2       broom_0.5.1         
##  [82] ggridges_0.5.1       evaluate_0.13        shinyBS_0.61        
##  [85] yaml_2.2.0           npsurv_0.4-0         knitr_1.21          
##  [88] bit64_0.9-7          fitdistrplus_1.0-14  robustbase_0.93-3   
##  [91] caTools_1.17.1.1     randomForest_4.6-14  RANN_2.6.1          
##  [94] pbapply_1.4-0        nlme_3.1-137         mime_0.6            
##  [97] slam_0.1-44          xml2_1.2.0           hdf5r_1.0.0         
## [100] compiler_3.5.0       rstudioapi_0.9.0     png_0.1-7           
## [103] lsei_1.2-0           stringi_1.3.1        highr_0.7           
## [106] lattice_0.20-35      trimcluster_0.1-2.1  HSMMSingleCell_1.2.0
## [109] pillar_1.3.1         combinat_0.0-8       Rdpack_0.10-1       
## [112] lmtest_0.9-36        data.table_1.12.0    bitops_1.0-6        
## [115] gbRd_0.4-11          httpuv_1.5.1         R6_2.4.0            
## [118] latticeExtra_0.6-28  promises_1.0.1       KernSmooth_2.23-15  
## [121] gridExtra_2.3        codetools_0.2-15     MASS_7.3-51.1       
## [124] gtools_3.8.1         assertthat_0.2.0     withr_2.1.2         
## [127] qlcMatrix_0.9.7      diptest_0.75-7       doSNOW_1.0.16       
## [130] hms_0.4.2            grid_3.5.0           rpart_4.1-13        
## [133] class_7.3-14         rmarkdown_1.11       segmented_0.5-3.0   
## [136] Rtsne_0.15           lubridate_1.7.4      shiny_1.2.0         
## [139] base64enc_0.1-3